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revision 1.27 by cnh, Thu Oct 14 14:24:28 2004 UTC revision 1.45 by jmc, Wed May 11 18:58:02 2011 UTC
# Line 3  Line 3 
3    
4  %\section{Getting started}  %\section{Getting started}
5    
6  In this section, we describe how to use the model. In the first  We believe the best way to familiarize yourself with the
 section, we provide enough information to help you get started with  
 the model. We believe the best way to familiarize yourself with the  
7  model is to run the case study examples provided with the base  model is to run the case study examples provided with the base
8  version. Information on how to obtain, compile, and run the code is  version. Information on how to obtain, compile, and run the code is
9  found there as well as a brief description of the model structure  found here as well as a brief description of the model structure
10  directory and the case study examples.  The latter and the code  directory and the case study examples. Information is also provided
11  structure are described more fully in chapters  here on how to customize the code when you are ready to try implementing
12  \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in  the configuration you have in mind.  The code and algorithm
13  this section, we provide information on how to customize the code when  are described more fully in chapters \ref{chap:discretization} and
14  you are ready to try implementing the configuration you have in mind.  \ref{chap:sarch}.
15    
16  \section{Where to find information}  \section{Where to find information}
17  \label{sect:whereToFindInfo}  \label{sec:whereToFindInfo}
18    \begin{rawhtml}
19    <!-- CMIREDIR:whereToFindInfo: -->
20    \end{rawhtml}
21    
22  A web site is maintained for release 2 (``Pelican'') of MITgcm:  There is a web-archived support mailing list for the model that
 \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/pelican  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 Here you will find an on-line version of this document, a  
 ``browsable'' copy of the code and a searchable database of the model  
 and site, as well as links for downloading the model and  
 documentation, to data-sources, and other related sites.  
   
 There is also a web-archived support mailing list for the model that  
23  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
24  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
25  \begin{verbatim}  \begin{verbatim}
# Line 37  http://mitgcm.org/mailman/listinfo/mitgc Line 27  http://mitgcm.org/mailman/listinfo/mitgc
27  http://mitgcm.org/pipermail/mitgcm-support/  http://mitgcm.org/pipermail/mitgcm-support/
28  \end{verbatim}  \end{verbatim}
29  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
 Essentially all of the MITgcm web pages can be searched using a  
 popular web crawler such as Google or through our own search facility:  
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/htdig/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org  
   
   
30    
31  \section{Obtaining the code}  \section{Obtaining the code}
32  \label{sect:obtainingCode}  \label{sec:obtainingCode}
33    \begin{rawhtml}
34    <!-- CMIREDIR:obtainingCode: -->
35    \end{rawhtml}
36    
37  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
38  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 80  provide easy support for maintenance upd Line 63  provide easy support for maintenance upd
63  \end{enumerate}  \end{enumerate}
64    
65  \subsection{Method 1 - Checkout from CVS}  \subsection{Method 1 - Checkout from CVS}
66  \label{sect:cvs_checkout}  \label{sec:cvs_checkout}
67    
68  If CVS is available on your system, we strongly encourage you to use it. CVS  If CVS is available on your system, we strongly encourage you to use it. CVS
69  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
# Line 92  be set within your shell.  For a csh or Line 75  be set within your shell.  For a csh or
75  \begin{verbatim}  \begin{verbatim}
76  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
77  \end{verbatim}  \end{verbatim}
78  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
79    shells, put:
80  \begin{verbatim}  \begin{verbatim}
81  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
82  \end{verbatim}  \end{verbatim}
# Line 108  You only need to do a ``cvs login'' once Line 92  You only need to do a ``cvs login'' once
92    
93  To obtain the latest sources type:  To obtain the latest sources type:
94  \begin{verbatim}  \begin{verbatim}
95  % cvs co MITgcm  % cvs co -P MITgcm
96  \end{verbatim}  \end{verbatim}
97  or to get a specific release type:  or to get a specific release type:
98  \begin{verbatim}  \begin{verbatim}
99  % cvs co -P -r checkpoint52i_post  MITgcm  % cvs co -P -r checkpoint52i_post MITgcm
100  \end{verbatim}  \end{verbatim}
101    The CVS command ``\texttt{cvs co}'' is the abreviation of the full-name
102    ``\texttt{cvs checkout}'' command and using the option ``-P'' (\texttt{cvs co -P})
103    will prevent to download unnecessary empty directories.
104    
105  The MITgcm web site contains further directions concerning the source  The MITgcm web site contains further directions concerning the source
106  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
107  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
108  development milestones:  development milestones:
109  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
110  \begin{verbatim}  \begin{verbatim}
111  http://mitgcm.org/source_code.html  http://mitgcm.org/viewvc/MITgcm/MITgcm/
112  \end{verbatim}  \end{verbatim}
113  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
114    
# Line 147  of CVS aliases Line 135  of CVS aliases
135    \label{tab:cvsModules}    \label{tab:cvsModules}
136  \end{table}  \end{table}
137    
138  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
139  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
140  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
141  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
142  track of your file versions with respect to the repository. Don't edit  track of your file versions with respect to the repository. Don't edit
143  the files in \textit{CVS}!  You can also use CVS to download code  the files in \texttt{CVS}!  You can also use CVS to download code
144  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
145  MITgcm code can be found  MITgcm code can be found
146  \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/public/using_cvs.html" target="idontexist"> \end{rawhtml}
147  here  here
148  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
149  .  .
# Line 164  It is important to note that the CVS ali Line 152  It is important to note that the CVS ali
152  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
153  they create can be changed to a different name following the check-out:  they create can be changed to a different name following the check-out:
154  \begin{verbatim}  \begin{verbatim}
155     %  cvs co MITgcm_verif_basic     %  cvs co -P MITgcm_verif_basic
156     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
157  \end{verbatim}  \end{verbatim}
158    
   
 \subsection{Method 2 - Tar file download}  
 \label{sect:conventionalDownload}  
   
 If you do not have CVS on your system, you can download the model as a  
 tar file from the web site at:  
 \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/download/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 The tar file still contains CVS information which we urge you not to  
 delete; even if you do not use CVS yourself the information can help  
 us if you should need to send us your copy of the code.  If a recent  
 tar file does not exist, then please contact the developers through  
 the  
 \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 MITgcm-support@mitgcm.org  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
   
159  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
160    
161  If you already have an earlier version of the code you can ``upgrade''  If you already have an earlier version of the code you can ``upgrade''
# Line 199  your copy instead of downloading the ent Line 166  your copy instead of downloading the ent
166  \end{verbatim}  \end{verbatim}
167  and then issue the cvs update command such as:  and then issue the cvs update command such as:
168  \begin{verbatim}  \begin{verbatim}
169  % cvs -q update -r checkpoint52i_post -d -P  % cvs -q update -d -P -r checkpoint52i_post
170  \end{verbatim}  \end{verbatim}
171  This will update the ``tag'' to ``checkpoint52i\_post'', add any new  This will update the ``tag'' to ``checkpoint52i\_post'', add any new
172  directories (-d) and remove any empty directories (-P). The -q option  directories (-d) and remove any empty directories (-P). The -q option
# Line 245  have run into a problem for which ``we h Line 212  have run into a problem for which ``we h
212  latest code'' and we haven't made a ``tag'' or ``release'' since that  latest code'' and we haven't made a ``tag'' or ``release'' since that
213  patch then you'll need to get the latest code:  patch then you'll need to get the latest code:
214  \begin{verbatim}  \begin{verbatim}
215  % cvs -q update -A -d -P  % cvs -q update -d -P -A
216  \end{verbatim}  \end{verbatim}
217  Unlike, the ``check-out'' and ``update'' procedures above, there is no  Unlike, the ``check-out'' and ``update'' procedures above, there is no
218  ``tag'' or release name. The -A tells CVS to upgrade to the  ``tag'' or release name. The -A tells CVS to upgrade to the
# Line 255  that you may only have part of a patch. Line 222  that you may only have part of a patch.
222  also means we can't tell what version of the code you are working  also means we can't tell what version of the code you are working
223  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
224    
225    \subsection{Method 2 - Tar file download}
226    \label{sec:conventionalDownload}
227    
228    If you do not have CVS on your system, you can download the model as a
229    tar file from the web site at:
230    \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
231    \begin{verbatim}
232    http://mitgcm.org/download/
233    \end{verbatim}
234    \begin{rawhtml} </A> \end{rawhtml}
235    The tar file still contains CVS information which we urge you not to
236    delete; even if you do not use CVS yourself the information can help
237    us if you should need to send us your copy of the code.  If a recent
238    tar file does not exist, then please contact the developers through
239    the
240    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
241    MITgcm-support@mitgcm.org
242    \begin{rawhtml} </A> \end{rawhtml}
243    mailing list.
244    
245  \section{Model and directory structure}  \section{Model and directory structure}
246    \begin{rawhtml}
247    <!-- CMIREDIR:directory_structure: -->
248    \end{rawhtml}
249    
250  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
251  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 263  framework for grid-point models. MITgcmU Line 253  framework for grid-point models. MITgcmU
253  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
254  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
255  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
256  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
257  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
258  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
259  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
260  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
261  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
262  part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is  part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
263  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
264  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
265  structure).  structure).
266    
267  \begin{itemize}  \begin{itemize}
268    
269  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{doc}: contains brief documentation notes.
   default directory in which to compile the code.  
     
 \item \textit{diags}: contains the code relative to time-averaged  
   diagnostics. It is subdivided into two subdirectories \textit{inc}  
   and \textit{src} that contain include files (*.\textit{h} files) and  
   Fortran subroutines (*.\textit{F} files), respectively.  
   
 \item \textit{doc}: contains brief documentation notes.  
     
 \item \textit{eesupp}: contains the execution environment source code.  
   Also subdivided into two subdirectories \textit{inc} and  
   \textit{src}.  
270        
271  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{eesupp}: contains the execution environment source code.
272    default directory in which to execute the code.    Also subdivided into two subdirectories \texttt{inc} and
273      \texttt{src}.
274      
275    \item \texttt{model}: this directory contains the main source code.
276      Also subdivided into two subdirectories \texttt{inc} and
277      \texttt{src}.
278        
279  \item \textit{model}: this directory contains the main source code.  \item \texttt{pkg}: contains the source code for the packages. Each
280    Also subdivided into two subdirectories \textit{inc} and    package corresponds to a subdirectory. For example, \texttt{gmredi}
   \textit{src}.  
     
 \item \textit{pkg}: contains the source code for the packages. Each  
   package corresponds to a subdirectory. For example, \textit{gmredi}  
281    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
282    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
283    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap:packagesI}.
284        
285  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
286    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
287    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
288    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
289    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
290    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
291      This directory also contains the subdirectory build\_options, which
292      contains the `optfiles' with the compiler options for the different
293      compilers and machines that can run MITgcm.
294        
295  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
296    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
297    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
298    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
299    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
300    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
301    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
302    model output.    model output. The subdirectory exch2 contains the code needed for
303        the exch2 package to work with different combinations of domain
304  \item \textit{verification}: this directory contains the model    decompositions.
   examples. See section \ref{sect:modelExamples}.  
   
 \end{itemize}  
   
 \section[MITgcm Example Experiments]{Example experiments}  
 \label{sect:modelExamples}  
   
 %% a set of twenty-four pre-configured numerical experiments  
   
 The MITgcm distribution comes with more than a dozen pre-configured  
 numerical experiments. Some of these example experiments are tests of  
 individual parts of the model code, but many are fully fledged  
 numerical simulations. A few of the examples are used for tutorial  
 documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  
 The other examples follow the same general structure as the tutorial  
 examples. However, they only include brief instructions in a text file  
 called {\it README}.  The examples are located in subdirectories under  
 the directory \textit{verification}. Each example is briefly described  
 below.  
   
 \subsection{Full list of model examples}  
   
 \begin{enumerate}  
     
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with  
   free-surface). This experiment is described in detail in section  
   \ref{sect:eg-baro}.  
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment  
   is described in detail in section \ref{sect:eg-baroc}.  
     
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in  
   section \ref{sect:eg-global}.  
     
 \item \textit{exp4} - Flow over a Gaussian bump in open-water or  
   channel with open boundaries.  
     
 \item \textit{exp5} - Inhomogenously forced ocean convection in a  
   doubly periodic box.  
   
 \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \textit{internal wave} - Ocean internal wave forced by open  
   boundary conditions.  
     
 \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  
   scheme; 1 month integration  
     
 \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing on the cubed sphere.  
     
 \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
   Global Zonal Mean configuration, 1x64x5 resolution.  
     
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  
   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).  
     
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  
   physics. 3D Equatorial Channel configuration.  
     
 \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  
   Global configuration, on latitude longitude grid with 128x64x5 grid  
   points ($2.8^\circ{\rm degree}$ resolution).  
     
 \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  
   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  
   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{advect\_cs} Two-dimensional passive advection test on  
   cube sphere grid.  
     
 \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{carbon} Simple passive tracer experiment. Includes  
   derivative calculation. Described in detail in section  
   \ref{sect:eg-carbon-ad}.  
   
 \item \textit{flt\_example} Example of using float package.  
     
 \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  
   boundary conditions and poles.  
   
 \item \textit{global\_ocean\_pressure} Global circulation in pressure  
   coordinate (non-Boussinesq ocean model). Described in detail in  
   section \ref{sect:eg-globalpressure}.  
     
 \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  
   sphere grid.  
   
 \end{enumerate}  
   
 \subsection{Directory structure of model examples}  
   
 Each example directory has the following subdirectories:  
   
 \begin{itemize}  
 \item \textit{code}: contains the code particular to the example. At a  
   minimum, this directory includes the following files:  
   
   \begin{itemize}  
   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to  
     the ``execution environment'' part of the code. The default  
     version is located in \textit{eesupp/inc}.  
     
   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to  
     the ``numerical model'' part of the code. The default version is  
     located in \textit{model/inc}.  
     
   \item \textit{code/SIZE.h}: declares size of underlying  
     computational grid.  The default version is located in  
     \textit{model/inc}.  
   \end{itemize}  
305        
306    In addition, other include files and subroutines might be present in  \item \texttt{verification}: this directory contains the model
307    \textit{code} depending on the particular experiment. See Section 2    examples. See section \ref{sec:modelExamples}.
   for more details.  
     
 \item \textit{input}: contains the input data files required to run  
   the example. At a minimum, the \textit{input} directory contains the  
   following files:  
308    
309    \begin{itemize}  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
   \item \textit{input/data}: this file, written as a namelist,  
     specifies the main parameters for the experiment.  
310        
311    \item \textit{input/data.pkg}: contains parameters relative to the  \item \texttt{lsopt}: Line search code used for optimization.
     packages used in the experiment.  
312        
313    \item \textit{input/eedata}: this file contains ``execution  \item \texttt{optim}: Interface between MITgcm and line search code.
     environment'' data. At present, this consists of a specification  
     of the number of threads to use in $X$ and $Y$ under multithreaded  
     execution.  
   \end{itemize}  
314        
   In addition, you will also find in this directory the forcing and  
   topography files as well as the files describing the initial state  
   of the experiment.  This varies from experiment to experiment. See  
   section 2 for more details.  
   
 \item \textit{results}: this directory contains the output file  
   \textit{output.txt} produced by the simulation example. This file is  
   useful for comparison with your own output when you run the  
   experiment.  
315  \end{itemize}  \end{itemize}
316    
 Once you have chosen the example you want to run, you are ready to  
 compile the code.  
   
317  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
318  \label{sect:buildingCode}  \label{sec:buildingCode}
319    \begin{rawhtml}
320  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
321  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
322  compiler and optimization options and also figures out any file  
323  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
324  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
325    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
326    file dependencies. We supply a script (\texttt{genmake2}), described
327    in section \ref{sec:genmake}, that automatically creates the
328    \texttt{Makefile} for you. You then need to build the dependencies and
329  compile the code.  compile the code.
330    
331  As an example, let's assume that you want to build and run experiment  As an example, assume that you want to build and run experiment
332  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
333  actually do this but here let's build the code in  actually do this but here let's build the code in
334  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
335  \begin{verbatim}  \begin{verbatim}
336  % cd verification/exp2/input  % cd verification/exp2/build
337  \end{verbatim}  \end{verbatim}
338  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
339  \begin{verbatim}  \begin{verbatim}
340  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
341  \end{verbatim}  \end{verbatim}
342  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
343  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
344    
345  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
346  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
347  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
348  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
349    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
350  may have to create a new ``optfile'' in order to specify the exact  circumstances, a user may have to create a new ``optfile'' in order to
351  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
352  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
353  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
354  mimic their syntax.  ``optfiles'' and mimic their syntax.
355    
356  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
357  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
358  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
359  architectures) to the  architectures) to the
360  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
361  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
362  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
363  list.  list.
364    
365  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
366  \begin{verbatim}  \begin{verbatim}
367  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
368  \end{verbatim}  \end{verbatim}
369    
370  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
371    dependencies with the command:
372  \begin{verbatim}  \begin{verbatim}
373  % make depend  % make depend
374  \end{verbatim}  \end{verbatim}
375  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
376  upon which other files depend. The purpose of this is to reduce  list of files upon which other files depend. The purpose of this is to
377  re-compilation if and when you start to modify the code. The {\tt make  reduce re-compilation if and when you start to modify the code. The
378    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
379  directory.  this directory.  It is important to note that the {\tt make depend}
380    stage will occasionally produce warnings or errors since the
381    dependency parsing tool is unable to find all of the necessary header
382    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
383    is usually OK to ignore the warnings/errors and proceed to the next
384    step.
385    
386  Next compile the code:  Next one can compile the code using:
387  \begin{verbatim}  \begin{verbatim}
388  % make  % make
389  \end{verbatim}  \end{verbatim}
390  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
391  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
392  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
393    (shared multi-processor) systems, the build process can often be sped
394    up appreciably using the command:
395    \begin{verbatim}
396    % make -j 2
397    \end{verbatim}
398    where the ``2'' can be replaced with a number that corresponds to the
399    number of CPUs available.
400    
401  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
402  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sec:runModel}. Here, we can run the model by
403    first creating links to all the input files:
404    \begin{verbatim}
405    ln -s ../input/* .
406    \end{verbatim}
407    and then calling the executable with:
408  \begin{verbatim}  \begin{verbatim}
409  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
410  \end{verbatim}  \end{verbatim}
411  where we are re-directing the stream of text output to the file {\em  where we are re-directing the stream of text output to the file
412  output.txt}.  \texttt{output.txt}.
   
413    
414  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
415    
416  In the example above (section \ref{sect:buildingCode}) we built the  In the example above (section \ref{sec:buildingCode}) we built the
417  executable in the {\em input} directory of the experiment for  executable in the {\em input} directory of the experiment for
418  convenience. You can also configure and compile the code in other  convenience. You can also configure and compile the code in other
419  locations, for example on a scratch disk with out having to copy the  locations, for example on a scratch disk with out having to copy the
# Line 667  the one experiment: Line 517  the one experiment:
517    
518    
519  \subsection{Using \texttt{genmake2}}  \subsection{Using \texttt{genmake2}}
520  \label{sect:genmake}  \label{sec:genmake}
521    
522  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
523  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
524  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
525  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
526  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
527  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
528  relies upon a number of ``optfiles'' located in the  %relies upon a number of ``optfiles'' located in the
529  \texttt{tools/build\_options} directory.  %\texttt{tools/build\_options} directory.
530    \texttt{genmake2} parses information from the following sources:
531    \begin{description}
532    \item[-] a {\em gemake\_local} file if one is found in the current
533      directory
534    \item[-] command-line options
535    \item[-] an "options file" as specified by the command-line option
536      \texttt{--optfile=/PATH/FILENAME}
537    \item[-] a {\em packages.conf} file (if one is found) with the
538      specific list of packages to compile. The search path for
539      file {\em packages.conf} is, first, the current directory and
540      then each of the "MODS" directories in the given order (see below).
541    \end{description}
542    
543    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
544    
545  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
546  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 749  for inclusion.  Please send the file to Line 613  for inclusion.  Please send the file to
613  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
614  mailing list.  mailing list.
615    
616    \subsubsection{Command-line options:}
617    
618  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
619  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
620  obtained from:  obtained from:
# Line 771  The most important command-line options Line 637  The most important command-line options
637    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
638    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
639        
640  \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
641    set of packages to be used.  The normal order of precedence for    directories containing ``modifications''.  These directories contain
642    packages is as follows:    files with names that may (or may not) exist in the main MITgcm
643    \begin{enumerate}    source tree but will be overridden by any identically-named sources
644    \item If available, the command line (\texttt{--pdefault}) settings    within the ``MODS'' directories.
     over-rule any others.  
   
   \item Next, \texttt{genmake2} will look for a file named  
     ``\texttt{packages.conf}'' in the local directory or in any of the  
     directories specified with the \texttt{--mods} option.  
       
   \item Finally, if neither of the above are available,  
     \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.  
   \end{enumerate}  
645        
646      The order of precedence for this "name-hiding" is as follows:
647      \begin{itemize}
648      \item ``MODS'' directories (in the order given)
649      \item Packages either explicitly specified or provided by default
650        (in the order given)
651      \item Packages included due to package dependencies (in the order
652        that that package dependencies are parsed)
653      \item The "standard dirs" (which may have been specified by the
654        ``-standarddirs'' option)
655      \end{itemize}
656      
657    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
658      where package groups are defined. If not set, the package-groups
659      definition will be read from {\em pkg/pkg\_groups}.
660      It also contains the default list of packages (defined
661      as the group ``{\it default\_pkg\_list}'' which is used
662      when no specific package list ({\em packages.conf})
663      is found in current directory or in any "MODS" directory.
664    
665  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
666    used for packages.    used for packages.
667        
# Line 810  The most important command-line options Line 686  The most important command-line options
686    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
687    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
688        
 \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of  
   directories containing ``modifications''.  These directories contain  
   files with names that may (or may not) exist in the main MITgcm  
   source tree but will be overridden by any identically-named sources  
   within the ``MODS'' directories.  
     
   The order of precedence for this "name-hiding" is as follows:  
   \begin{itemize}  
   \item ``MODS'' directories (in the order given)  
   \item Packages either explicitly specified or provided by default  
     (in the order given)  
   \item Packages included due to package dependencies (in the order  
     that that package dependencies are parsed)  
   \item The "standard dirs" (which may have been specified by the  
     ``-standarddirs'' option)  
   \end{itemize}  
     
689  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
690    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
691    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sec:mpi-build}).
692        
693  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
694    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
# Line 852  The most important command-line options Line 711  The most important command-line options
711    
712    
713  \subsection{Building with MPI}  \subsection{Building with MPI}
714  \label{sect:mpi-build}  \label{sec:mpi-build}
715    
716  Building MITgcm to use MPI libraries can be complicated due to the  Building MITgcm to use MPI libraries can be complicated due to the
717  variety of different MPI implementations available, their dependencies  variety of different MPI implementations available, their dependencies
# Line 867  The steps for building MITgcm with MPI s Line 726  The steps for building MITgcm with MPI s
726        
727  \item Determine the locations of your MPI-enabled compiler and/or MPI  \item Determine the locations of your MPI-enabled compiler and/or MPI
728    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
729    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sec:genmake}.  One can start with one of the examples in:
730    \begin{rawhtml} <A    \begin{rawhtml} <A
731      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
732    \end{rawhtml}    \end{rawhtml}
733    \begin{center}    \begin{center}
734      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 902  The steps for building MITgcm with MPI s Line 761  The steps for building MITgcm with MPI s
761    \end{itemize}    \end{itemize}
762        
763  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
764    (see Section \ref{sect:genmake}) using commands such as:    (see Section \ref{sec:genmake}) using commands such as:
765  {\footnotesize \begin{verbatim}  {\footnotesize \begin{verbatim}
766    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
767    %  make depend    %  make depend
# Line 920  The steps for building MITgcm with MPI s Line 779  The steps for building MITgcm with MPI s
779    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
780    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
781    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
782      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
783    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
784    at:    at:
785    \begin{rawhtml} <A    \begin{rawhtml} <A
786      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
787      \end{rawhtml}
788      {\footnotesize \tt
789        http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
790      \begin{rawhtml} </A> \end{rawhtml}
791      or at:
792      \begin{rawhtml} <A
793        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
794    \end{rawhtml}    \end{rawhtml}
795    {\footnotesize \tt    {\footnotesize \tt
796      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
797    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
798    
799  \end{enumerate}  \end{enumerate}
# Line 948  the GNU g77 compiler and the mpich MPI l Line 814  the GNU g77 compiler and the mpich MPI l
814         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
815  \end{verbatim} }  \end{verbatim} }
816    
   
   
817  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
818  \label{sect:runModel}  \label{sec:runModel}
819    \begin{rawhtml}
820    <!-- CMIREDIR:runModel: -->
821    \end{rawhtml}
822    
823  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sec:buildingCode})
824  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
825  local directory.  local directory.
826    
827  To run the model as a single process (ie. not in parallel) simply  To run the model as a single process (\textit{ie.} not in parallel)
828  type:  simply type:
829  \begin{verbatim}  \begin{verbatim}
830  % ./mitgcmuv  % ./mitgcmuv
831  \end{verbatim}  \end{verbatim}
# Line 968  do!). The above command will spew out ma Line 835  do!). The above command will spew out ma
835  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
836  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
837  etc. It is worth keeping this text output with the binary output so we  etc. It is worth keeping this text output with the binary output so we
838  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
839  \begin{verbatim}  \begin{verbatim}
840  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
841  \end{verbatim}  \end{verbatim}
842    In the event that the model encounters an error and stops, it is very
843  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
844  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
845  your {\em output.txt} with this one to check that the set-up works.  
846    For the example experiments in \texttt{verification}, an example of the
847    output is kept in \texttt{results/output.txt} for comparison. You can
848    compare your \texttt{output.txt} with the corresponding one for that
849    experiment to check that the set-up works.
850    
851    
852    
853  \subsection{Output files}  \subsection{Output files}
854    
855  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
856  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
857    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
858    both as determined by \texttt{code/packages.conf}) and the run-time
859    flags set (in \texttt{input/data.pkg}), the following output may
860    appear.
861    
862    
863    \subsubsection{MDSIO output files}
864    
865    The ``traditional'' output files are generated by the \texttt{mdsio}
866    package.  At a minimum, the instantaneous ``state'' of the model is
867    written out, which is made of the following files:
868    
869  \begin{itemize}  \begin{itemize}
870  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
871  0 $ eastward).    and positive eastward).
872    
873  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
874  and $> 0$ northward).    (m/s and positive northward).
875    
876  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
877  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
878  i.e. downward).    towards increasing pressure i.e. downward).
879    
880  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
881  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
882    
883  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
884  (g/kg).    vapor (g/kg).
885    
886  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
887  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
888  \end{itemize}  \end{itemize}
889    
890  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
891  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
892  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
893    
894  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
895    
896  \begin{itemize}  \begin{itemize}
897  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
898  \end{itemize}  \end{itemize}
899    
900  is written out. This file represents the state of the model in a condensed  is written out. This file represents the state of the model in a condensed
# Line 1020  form and is used for restarting the inte Line 902  form and is used for restarting the inte
902  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
903    
904  \begin{itemize}  \begin{itemize}
905  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
906  \end{itemize}  \end{itemize}
907    
908  containing the D-grid velocity data and that has to be written out as well  containing the D-grid velocity data and that has to be written out as well
909  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
910  as the pickup files but are named differently. Their name contain the chain  as the pickup files but are named differently. Their name contain the chain
911  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
912  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
913  output to save disk space during long integrations.  output to save disk space during long integrations.
914    
915    \subsubsection{MNC output files}
916    
917    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
918    is usually (though not necessarily) placed within a subdirectory with
919    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
920    
921  \subsection{Looking at the output}  \subsection{Looking at the output}
922    
923  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
924  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
925  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
926  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
927  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
928  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
929  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
930  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
931  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
932  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
933  the data. Look at the comments inside the script to see how to use it.  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
934    reads the data. Look at the comments inside the script to see how to
935    use it.
936    
937  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
938  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 949  Some examples of reading and visualizing
949  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
950  \end{verbatim}  \end{verbatim}
951    
952    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
953    they are described in Section \ref{sec:pkg:mnc}.
954    
955    The MNC output files are all in the ``self-describing'' netCDF
956    format and can thus be browsed and/or plotted using tools such as:
957    \begin{itemize}
958    \item \texttt{ncdump} is a utility which is typically included
959      with every netCDF install:
960      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
961    \begin{verbatim}
962    http://www.unidata.ucar.edu/packages/netcdf/
963    \end{verbatim}
964      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
965      binaries into formatted ASCII text files.
966    
967    \item \texttt{ncview} utility is a very convenient and quick way
968      to plot netCDF data and it runs on most OSes:
969      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
970    \begin{verbatim}
971    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
972    \end{verbatim}
973      \begin{rawhtml} </A> \end{rawhtml}
974      
975    \item MatLAB(c) and other common post-processing environments provide
976      various netCDF interfaces including:
977      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
978    \begin{verbatim}
979    http://mexcdf.sourceforge.net/
980    \end{verbatim}
981      \begin{rawhtml} </A> \end{rawhtml}
982      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
983    \begin{verbatim}
984    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
985    \end{verbatim}
986      \begin{rawhtml} </A> \end{rawhtml}
987    \end{itemize}
988    
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